PT - JOURNAL ARTICLE AU - Kathryn Geiger-Schuller AU - Basak Eraslan AU - Olena Kuksenko AU - Kushal K. Dey AU - Karthik A. Jagadeesh AU - Pratiksha I. Thakore AU - Ozge Karayel AU - Andrea R. Yung AU - Anugraha Rajagopalan AU - Ana M Meireles AU - Karren Dai Yang AU - Liat Amir-Zilberstein AU - Toni Delorey AU - Devan Phillips AU - Raktima Raychowdhury AU - Christine Moussion AU - Alkes L. Price AU - Nir Hacohen AU - John G. Doench AU - Caroline Uhler AU - Orit Rozenblatt-Rosen AU - Aviv Regev TI - Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq AID - 10.1101/2023.01.23.525198 DP - 2023 Jan 01 TA - bioRxiv PG - 2023.01.23.525198 4099 - http://biorxiv.org/content/early/2023/01/24/2023.01.23.525198.short 4100 - http://biorxiv.org/content/early/2023/01/24/2023.01.23.525198.full AB - E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comĪ²VAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.Competing Interest StatementSee Competing Interests Statement in manuscript for full disclosures. A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas, and until July 31, 2020 was an S.A.B. member of Thermo Fisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics and Asimov. K.R.G., B.E., P.I.T., O.K., A.R.Y., An.R., A.M.M., D.P., C.M., O.R.R., and A.R. are employees of Genentech and have equity in Roche. A.R., O.R.R., K.G.S., B.E., and P.I.T. are inventors on patents from the Broad related to single cell genomics / Perturb-Seq or this manuscript. JGD consults for Microsoft Research, Abata Therapeutics, Servier, Maze Therapeutics, BioNTech, Sangamo, and Pfizer. JGD consults for and has equity in Tango Therapeutics. JGD serves as a paid scientific advisor to the Laboratory for Genomics Research, funded in part by GlaxoSmithKline. JGD receives funding support from the Functional Genomics Consortium including Abbvie, Bristol Myers Squibb, Janssen, Merck, and Vir Biotechnology.